Hi we tried to run the workflow at the repository:
If we run the workflow with cwltool using the job description in:
with cwltool everything works. But when we run it with toil-cwl-runner we get an error:
WARNING:toil.leader:h/Z/job39e5364q File "<string>", line 1, in <module>
WARNING:toil.leader:h/Z/job39e5364q cwltool.errors.WorkflowException: steps/DP3.GenericStep.cwl:11:5: Missing required input parameter 'parameters_input'
The cwltool version is 1.0.20190906054215 while toil version is 3.21.0a1.
How is that possible?
Does it have to do with the concatenation of the JSON output?
Hello @Mattia_Mancini and thanks for talking to us here.
toil-cwl-runner currently has some bugs with default values and I think you have also hit the same bug
Thanks, we were able to work around this bug.